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| author | Thomas White <taw@physics.org> | 2013-05-30 10:48:44 -0700 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2013-05-30 10:48:44 -0700 |
| commit | aab623d73967e7570f92da5b84bac598e2273d6d (patch) | |
| tree | 98d4aa2665236111cbacfa1387c9c252cd69d494 | |
| parent | 494de86c5b3e15d0f006c6c1feb40643d74dbc24 (diff) | |
indexamajig: Get rid of --use-saturated, because it's now the default
| -rw-r--r-- | doc/man/indexamajig.1 | 4 | ||||
| -rw-r--r-- | src/indexamajig.c | 5 |
2 files changed, 4 insertions, 5 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 7ab68ba5..87657ac5 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -302,9 +302,9 @@ with old scripts because this option selects the behaviour which is now the default. .PD 0 -.IP \fB--use-saturated\fR +.IP \fB--no-use-saturated\fR .PD -Normally, peaks which contain one or more pixels above max_adu (defined in the detector geometry file) will not be used for indexing. Using this option skips this check, possibly improving the indexing rate if there is a large proportion of saturated peaks. +Normally, peaks which contain one or more pixels above max_adu (defined in the detector geometry file) will be used for indexing (but not used in the final integration - see the section on peak integration above). Using this option causes saturated peaks to be ignored completely. The opposite is \fB--use-saturated\fR, which is the default. .PD 0 .IP \fB--no-revalidate\fR diff --git a/src/indexamajig.c b/src/indexamajig.c index dc244866..67e9a7c4 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -139,9 +139,7 @@ static void show_help(const char *s) " --no-check-prefix Don't attempt to correct the --prefix.\n" " --closer-peak Don't integrate from the location of a nearby peak\n" " instead of the predicted spot. Don't use.\n" -" --use-saturated During the initial peak search, don't reject\n" -" peaks which contain pixels above max_adu.\n" -" --integrate-saturated During the final integration stage, don't reject\n" +" --no-use-saturated During the initial peak search, reject\n" " peaks which contain pixels above max_adu.\n" " --no-revalidate Don't re-integrate and check HDF5 peaks for\n" " validity.\n" @@ -239,6 +237,7 @@ int main(int argc, char *argv[]) {"no-refls-in-stream", 0, &iargs.stream_refls, 0}, {"integrate-saturated",0, &iargs.integrate_saturated,1}, {"use-saturated", 0, &iargs.use_saturated, 1}, + {"no-use-saturated", 0, &iargs.use_saturated, 0}, {"no-revalidate", 0, &iargs.no_revalidate, 1}, /* Long-only options with arguments */ |